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Advanced features

autoBUSTER Documentation : Advanced features

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Contents


The .autoBUSTER system of files and advanced command-line syntax

Some advanced features that are not available through command line switches (see also 'refine -h' for a complete list of those) can be set using two mechanisms:
  1. (preferred) a command line argument of the form

    parameter="value"

  2. To change some installation-wide defaults, a file .autoBUSTER can be placed into the same directory where the 'refine' binary is placed after installation, e.g. $BDG_home/autoBUSTER/bin/linux/.autoBUSTER. A file $HOME/.autoBUSTER (to set user-specific options) or ./.autoBUSTER (to set project-specific options) can also be used. The syntax of these files is:

    Additionally, the environment variable $MyDotAutobuster can point to a file that will be used on top of the above hard-coded files.

Some of these options are described below: if a refinement doesn't behave as expected, or some additional control is required, please let us know: it is possible that some parameters are already available to do what you need.


The macro feature

To group related sets of parameters and to give easier access to refinement strategies for specific situations, a macro feature has been introduced. This uses simple ASCII text-files of the format
# Comment line(s) explaining the purpose
# of this macro
__args="-adding -command -line -arguments"
param1=val1
# other comment (ignored)
param2="valA valB"

Notes:


Grouped list of parameters

The list of parameters (sorted alphabetical) is given in Appendix 1.


Some parameters most likely to be of interest

This list is probably not complete (see above for a nearly complete list): if you feel the need for doing something slightly different, please get in contact with us (we might be already able to show you how this could be done).

  1. There are two programs available for adding/removing/updating waters: arp_waters (from the CCP4 suite - especially written for updating of the water/solvent structure) or pkmaps (from SHARP/autoSHARP). The default (for the moment) is to use pkmaps (which might be better when the goal is to explain positive difference density through 'waters').

    There is also the possibility to use an external program/script for this task: in that case the absolute path to this program/script should be given. This script will be given the arguments

    1. current PDB file
    2. MTZ file for 2Fo-Fc map (columns 2FOFCWT/PH2FOFCWT)
    3. MTZ file for Fo-Fc map (columns FOFCWT/PHFOFCWT)
    4. (sub-)directory for this run (e.g. for writing additional or temporary output to)
    5. name of output PDB file (should be a copy of the input PDB file as much as possible, with only the waters updated)
    6. (optional) PDB file with coordinates of waters that have already been removed in previous steps

    The parameter WaterUpdateProgram can be either set to "PKMAPS", "ARP_WATERS" or the absolute path of a user-supplied program/script.

    The levels for adding removing waters can be controlled using the parameters WaterFindSigma, WaterRemoveSigma and WaterRemoveMerge

    To completely switch off the update of solvent structure (or delay if for a few initial BIG cycles) see the -noWAT command line switch.

  2. The resolution limits where different B-factor refinement schemes are used can be set with the parameters UseBrefNoneFrom, UseBrefGroupFrom and UseBrefMcScFrom. To enforce a specific B-factor refinement scheme, the command line flag -B can be used.

    The parameters to -B are

    individualRefine one B-factor per atom. This is almost always the right option to use
    group-mcscRefine one B-factor shift for each main chain (N, C, CA, O) and another for the side chain
    group-resRefine one B-factor shift for each residue
    NoneDo not change the B-factors from the input file

    Note that BUSTER refines B-factor shifts within groups; it is therefore important to use the InitialiseBiso option when using grouped B refinement. Either pick an initial B-factor that you think appropriate, or use InitialiseBiso=wilson.

    If a grouped B-factor refinement scheme is selected, the restraint in temperature factors of bonded atoms (BCORREL) could be switched off using the GeometryWeight_bcorrel parameter.

  3. The various (relative) weights on geometric restraints can be set with the parameters GeometryWeight_bond, GeometryWeight_angle, GeometryWeight_torsion, GeometryWeight_plane, GeometryWeight_trigonal, GeometryWeight_chiral, GeometryWeight_contact, GeometryWeight_bcorrel, GeometryWeight_ncs, GeometryWeight_improper, GeometryWeight_pseudo and GeometryWeight_ideal.

  4. To change the starting X-ray weight (and associated minimum and maximum allowed values), use the XrayWeight_start, XrayWeight_min and XrayWeight_max parameters. autoBUSTER will automatically adjust the X-ray weight, unless told not to do so.

  5. GELLY has its own set of additional command-line arguments that can be added using the BusterExtraArgs parameter.

  6. controlling output formatting can be done by setting the environment variable $autoBUSTER_NO_HIGHLIGHT to a non-empty value. This will supress the use of certain escape sequences to create bold, underline or italic characters. Please note that this needs to be set as an environment variable, rather than an option on the refine command line!

Last modification: 24.01.11